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Bahti A, Telfah A, Lambert J, Hergenröder R, Suter D. Optimal control pulses for subspectral editing in low field NMR. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2021; 328:106993. [PMID: 34029798 DOI: 10.1016/j.jmr.2021.106993] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Revised: 03/14/2021] [Accepted: 04/26/2021] [Indexed: 06/12/2023]
Abstract
Low field NMR is an inexpensive and low footprint technique to obtain physical, chemical, electronic and structural information on small molecules, but suffers from poor spectral dispersion, especially when applied to the analysis of mixtures. Subspectral editing employing optimal control pulses is a suitable approach to cope with the severe signal superpositions in complex mixture spectra at low field. In this contribution, the use of optimal control pulses is demonstrated to be feasible at a field strength as low as 0.5 T. The optimal control pulse shapes were calculated using the Krotov algorithm. Downsizing the complexity of the algorithm from exponential to polynomial is shown to be possible by using a system approach with each system corresponding to a (small) molecule. In this way compound selective excitation pulses can be calculated. The signals of substructures of the cyclopentenone molecule were excited using optimal control pulses calculated by the Krotov algorithm demonstrating the feasibility of subspectral editing. Likewise, for a mixture of benzoic acid and alanine, editing of the signals of either benzoic acid or alanine employing optimal control pulses was shown to be possible. The obtained results are very promising and can be extended to the targeted analysis of complex mixtures such as biofluids or metabolic samples at low field strengths opening access for benchtop NMR to point of care settings.
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Affiliation(s)
- A Bahti
- Leibniz-Institut für Analytische Wissenschaften - ISAS - e.V., 44139 Dortmund, Germany; Experimental Physics III, TU Dortmund University, 44227 Dortmund, Germany.
| | - A Telfah
- Leibniz-Institut für Analytische Wissenschaften - ISAS - e.V., 44139 Dortmund, Germany
| | - J Lambert
- Leibniz-Institut für Analytische Wissenschaften - ISAS - e.V., 44139 Dortmund, Germany
| | - R Hergenröder
- Leibniz-Institut für Analytische Wissenschaften - ISAS - e.V., 44139 Dortmund, Germany.
| | - D Suter
- Experimental Physics III, TU Dortmund University, 44227 Dortmund, Germany
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HR-MAS NMR Based Quantitative Metabolomics in Breast Cancer. Metabolites 2019; 9:metabo9020019. [PMID: 30678289 PMCID: PMC6410210 DOI: 10.3390/metabo9020019] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2018] [Revised: 01/17/2019] [Accepted: 01/18/2019] [Indexed: 01/23/2023] Open
Abstract
High resolution magic-angle spinning (HR-MAS) nuclear magnetic resonance (NMR) spectroscopy is increasingly used for profiling of breast cancer tissue, delivering quantitative information for approximately 40 metabolites. One unique advantage of the method is that it can be used to analyse intact tissue, thereby requiring only minimal sample preparation. Importantly, since the method is non-destructive, it allows further investigations of the same specimen using for instance transcriptomics. Here, we discuss technical aspects critical for a successful analysis—including sample handling, measurement conditions, pulse sequences for one- and two dimensional analysis, and quantification methods—and summarize available studies, with a focus on significant associations of metabolite levels with clinically relevant parameters.
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Vinding MS, Guérin B, Vosegaard T, Nielsen NC. Local SAR, global SAR, and power-constrained large-flip-angle pulses with optimal control and virtual observation points. Magn Reson Med 2017; 77:374-384. [PMID: 26715084 PMCID: PMC4929033 DOI: 10.1002/mrm.26086] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2015] [Revised: 11/03/2015] [Accepted: 11/23/2015] [Indexed: 11/11/2022]
Abstract
PURPOSE To present a constrained optimal-control (OC) framework for designing large-flip-angle parallel-transmit (pTx) pulses satisfying hardware peak-power as well as regulatory local and global specific-absorption-rate (SAR) limits. The application is 2D and 3D spatial-selective 90° and 180° pulses. THEORY AND METHODS The OC gradient-ascent-pulse-engineering method with exact gradients and the limited-memory Broyden-Fletcher-Goldfarb-Shanno method is proposed. Local SAR is constrained by the virtual-observation-points method. Two numerical models facilitated the optimizations, a torso at 3 T and a head at 7 T, both in eight-channel pTx coils and acceleration-factors up to 4. RESULTS The proposed approach yielded excellent flip-angle distributions. Enforcing the local-SAR constraint, as opposed to peak power alone, reduced the local SAR 7 and 5-fold with the 2D torso excitation and inversion pulse, respectively. The root-mean-square errors of the magnetization profiles increased less than 5% with the acceleration factor of 4. CONCLUSION A local and global SAR, and peak-power constrained OC large-flip-angle pTx pulse design was presented, and numerically validated for 2D and 3D spatial-selective 90° and 180° pulses at 3 T and 7 T. Magn Reson Med 77:374-384, 2017. © 2015 Wiley Periodicals, Inc.
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Affiliation(s)
- Mads S. Vinding
- Center of Insoluble Protein Structures (inSPIN), Interdisciplinary Nanoscience Center (iNANO) and Department of Chemistry, Aarhus University, Aarhus C, Denmark
| | - Bastien Guérin
- A.A. Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital, Charlestown, Massachusetts, USA
- Harvard Medical School, Boston, Massachusetts, USA
| | - Thomas Vosegaard
- Center of Insoluble Protein Structures (inSPIN), Interdisciplinary Nanoscience Center (iNANO) and Department of Chemistry, Aarhus University, Aarhus C, Denmark
| | - Niels Chr. Nielsen
- Center of Insoluble Protein Structures (inSPIN), Interdisciplinary Nanoscience Center (iNANO) and Department of Chemistry, Aarhus University, Aarhus C, Denmark
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Gogiashvili M, Edlund K, Gianmoena K, Marchan R, Brik A, Andersson JT, Lambert J, Madjar K, Hellwig B, Rahnenführer J, Hengstler JG, Hergenröder R, Cadenas C. Metabolic profiling of ob/ob mouse fatty liver using HR-MAS 1H-NMR combined with gene expression analysis reveals alterations in betaine metabolism and the transsulfuration pathway. Anal Bioanal Chem 2016; 409:1591-1606. [PMID: 27896396 DOI: 10.1007/s00216-016-0100-1] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2016] [Revised: 10/21/2016] [Accepted: 11/14/2016] [Indexed: 02/07/2023]
Abstract
Metabolic perturbations resulting from excessive hepatic fat accumulation are poorly understood. Thus, in this study, leptin-deficient ob/ob mice, a mouse model of fatty liver disease, were used to investigate metabolic alterations in more detail. Metabolites were quantified in intact liver tissues of ob/ob (n = 8) and control (n = 8) mice using high-resolution magic angle spinning (HR-MAS) 1H-NMR. In addition, after demonstrating that HR-MAS 1H-NMR does not affect RNA integrity, transcriptional changes were measured by quantitative real-time PCR on RNA extracted from the same specimens after HR-MAS 1H-NMR measurements. Importantly, the gene expression changes obtained agreed with those observed by Affymetrix microarray analysis performed on RNA isolated directly from fresh-frozen tissue. In total, 40 metabolites could be assigned in the spectra and subsequently quantified. Quantification of lactate was also possible after applying a lactate-editing pulse sequence that suppresses the lipid signal, which superimposes the lactate methyl resonance at 1.3 ppm. Significant differences were detected for creatinine, glutamate, glycine, glycolate, trimethylamine-N-oxide, dimethylglycine, ADP, AMP, betaine, phenylalanine, and uridine. Furthermore, alterations in one-carbon metabolism, supported by both metabolic and transcriptional changes, were observed. These included reduced demethylation of betaine to dimethylglycine and the reduced expression of genes coding for transsulfuration pathway enzymes, which appears to preserve methionine levels, but may limit glutathione synthesis. Overall, the combined approach is advantageous as it identifies changes not only at the single gene or metabolite level but also deregulated pathways, thus providing critical insight into changes accompanying fatty liver disease. Graphical abstract A Evaluation of RNA integrity before and after HR-MAS 1H-NMR of intact mouse liver tissue. B Metabolite concentrations and gene expression levels assessed in ob/ob (steatotic) and ob/+ (control) mice using HR-MAS 1H-NMR and qRT-PCR, respectively.
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Affiliation(s)
- Mikheil Gogiashvili
- Leibniz Institut für Analytische Wissenschaften - ISAS e.V., Bunsen-Kirchhoff-Strasse 11, 44139, Dortmund, Germany.
| | - Karolina Edlund
- Leibniz Research Centre for Working Environment and Human Factors (IfADo), Ardeystrasse 67, 44139, Dortmund, Germany
| | - Kathrin Gianmoena
- Leibniz Research Centre for Working Environment and Human Factors (IfADo), Ardeystrasse 67, 44139, Dortmund, Germany
| | - Rosemarie Marchan
- Leibniz Research Centre for Working Environment and Human Factors (IfADo), Ardeystrasse 67, 44139, Dortmund, Germany
| | - Alexander Brik
- Institute for Prevention and Occupational Medicine of the German Social Accident Insurance (IPA), Institute of the Ruhr-Universität Bochum, Bürkle-de-la-Camp-Platz 1, 44789, Bochum, Germany
| | - Jan T Andersson
- Institute of Inorganic and Analytical Chemistry, University of Münster, Corrensstrasse 30, 48149, Münster, Germany
| | - Jörg Lambert
- Leibniz Institut für Analytische Wissenschaften - ISAS e.V., Bunsen-Kirchhoff-Strasse 11, 44139, Dortmund, Germany
| | - Katrin Madjar
- Faculty of Statistics, TU Dortmund University, Mathematics Building, 44221, Dortmund, Germany
| | - Birte Hellwig
- Faculty of Statistics, TU Dortmund University, Mathematics Building, 44221, Dortmund, Germany
| | - Jörg Rahnenführer
- Faculty of Statistics, TU Dortmund University, Mathematics Building, 44221, Dortmund, Germany
| | - Jan G Hengstler
- Leibniz Research Centre for Working Environment and Human Factors (IfADo), Ardeystrasse 67, 44139, Dortmund, Germany
| | - Roland Hergenröder
- Leibniz Institut für Analytische Wissenschaften - ISAS e.V., Bunsen-Kirchhoff-Strasse 11, 44139, Dortmund, Germany
| | - Cristina Cadenas
- Leibniz Research Centre for Working Environment and Human Factors (IfADo), Ardeystrasse 67, 44139, Dortmund, Germany
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Edelhoff D, Walczak L, Frank F, Heil M, Schmitz I, Weichert F, Suter D. Measurement with microscopic MRI and simulation of flow in different aneurysm models. Med Phys 2015; 42:5661-70. [PMID: 26429240 DOI: 10.1118/1.4929758] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Abstract
PURPOSE The impact and the development of aneurysms depend to a significant degree on the exchange of liquid between the regular vessel and the pathological extension. A better understanding of this process will lead to improved prediction capabilities. The aim of the current study was to investigate fluid-exchange in aneurysm models of different complexities by combining microscopic magnetic resonance measurements with numerical simulations. In order to evaluate the accuracy and applicability of these methods, the fluid-exchange process between the unaltered vessel lumen and the aneurysm phantoms was analyzed quantitatively using high spatial resolution. METHODS Magnetic resonance flow imaging was used to visualize fluid-exchange in two different models produced with a 3D printer. One model of an aneurysm was based on histological findings. The flow distribution in the different models was measured on a microscopic scale using time of flight magnetic resonance imaging. The whole experiment was simulated using fast graphics processing unit-based numerical simulations. The obtained simulation results were compared qualitatively and quantitatively with the magnetic resonance imaging measurements, taking into account flow and spin-lattice relaxation. RESULTS The results of both presented methods compared well for the used aneurysm models and the chosen flow distributions. The results from the fluid-exchange analysis showed comparable characteristics concerning measurement and simulation. Similar symmetry behavior was observed. Based on these results, the amount of fluid-exchange was calculated. Depending on the geometry of the models, 7% to 45% of the liquid was exchanged per second. CONCLUSIONS The result of the numerical simulations coincides well with the experimentally determined velocity field. The rate of fluid-exchange between vessel and aneurysm was well-predicted. Hence, the results obtained by simulation could be validated by the experiment. The observed deviations can be caused by the noise in the measurement and by the limited resolution of the simulation. The resulting differences are small enough to allow reliable predictions of the flow distribution in vessels with stents and for pulsed blood flow.
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Affiliation(s)
- Daniel Edelhoff
- Experimental Physics III, TU Dortmund University, Otto-Hahn-Street 4, Dortmund 44227, Germany
| | - Lars Walczak
- Computer Science VII, TU Dortmund University, Otto-Hahn-Street 16, Dortmund 44227, Germany
| | - Frauke Frank
- Experimental Physics III, TU Dortmund University, Otto-Hahn-Street 4, Dortmund 44227, Germany
| | - Marvin Heil
- Experimental Physics III, TU Dortmund University, Otto-Hahn-Street 4, Dortmund 44227, Germany
| | - Inge Schmitz
- Institute for Pathology, Ruhr Universität Bochum, Bürkle-de-la-Camp-Platz 1, Bochum 44789, Germany
| | - Frank Weichert
- Computer Science VII, TU Dortmund University, Otto-Hahn-Street 16, Dortmund 44227, Germany
| | - Dieter Suter
- Experimental Physics III, TU Dortmund University, Otto-Hahn-Street 4, Dortmund 44227, Germany
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Holbach M, Lambert J, Johst S, Ladd ME, Suter D. Optimized selective lactate excitation with a refocused multiple-quantum filter. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2015; 255:34-38. [PMID: 25909643 DOI: 10.1016/j.jmr.2015.03.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2014] [Revised: 02/20/2015] [Accepted: 03/09/2015] [Indexed: 06/04/2023]
Abstract
Selective detection of lactate signals in in vivo MR spectroscopy with spectral editing techniques is necessary in situations where strong lipid or signals from other molecules overlap the desired lactate resonance in the spectrum. Several pulse sequences have been proposed for this task. The double-quantum filter SSel-MQC provides very good lipid and water signal suppression in a single scan. As a major drawback, it suffers from significant signal loss due to incomplete refocussing in situations where long evolution periods are required. Here we present a refocused version of the SSel-MQC technique that uses only one additional refocussing pulse and regains the full refocused lactate signal at the end of the sequence.
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Affiliation(s)
- Mirjam Holbach
- Experimental Physics III, TU Dortmund University, 44227 Dortmund, Germany.
| | - Jörg Lambert
- Leibniz Institut für Analytische Wissenschaften - ISAS e.V., 44139 Dortmund, Germany
| | - Sören Johst
- Erwin L. Hahn Institute for Magnetic Resonance Imaging, University Duisburg-Essen, 45141 Essen, Germany
| | - Mark E Ladd
- Erwin L. Hahn Institute for Magnetic Resonance Imaging, University Duisburg-Essen, 45141 Essen, Germany; Medical Physics in Radiology, German Cancer Research Center, 69120 Heidelberg, Germany
| | - Dieter Suter
- Experimental Physics III, TU Dortmund University, 44227 Dortmund, Germany
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